Lead finder: An approach to improve accuracy of protein− ligand docking, binding energy estimation, and virtual screening
An innovative molecular docking algorithm and three specialized high accuracy scoring
functions are introduced in the Lead Finder docking software. Lead Finder's algorithm for …
functions are introduced in the Lead Finder docking software. Lead Finder's algorithm for …
Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: the prediction accuracy of sampling power and scoring power
Z Wang, H Sun, X Yao, D Li, L Xu, Y Li… - Physical Chemistry …, 2016 - pubs.rsc.org
As one of the most popular computational approaches in modern structure-based drug
design, molecular docking can be used not only to identify the correct conformation of a …
design, molecular docking can be used not only to identify the correct conformation of a …
Receptor–ligand molecular docking
Docking methodology aims to predict the experimental binding modes and affinities of small
molecules within the binding site of particular receptor targets and is currently used as a …
molecules within the binding site of particular receptor targets and is currently used as a …
Ligand− protein database: Linking protein− ligand complex structures to binding data
O Roche, R Kiyama, CL Brooks - Journal of medicinal chemistry, 2001 - ACS Publications
In computational structure-based drug design, the scoring functions are the cornerstones to
the success of design/discovery. Many approaches have been explored to improve their …
the success of design/discovery. Many approaches have been explored to improve their …
Evaluation of Docking Target Functions by the Comprehensive Investigation of Protein‐Ligand Energy Minima
IV Oferkin, EV Katkova, AV Sulimov… - Advances in …, 2015 - Wiley Online Library
The adequate choice of the docking target function impacts the accuracy of the ligand
positioning as well as the accuracy of the protein‐ligand binding energy calculation. To …
positioning as well as the accuracy of the protein‐ligand binding energy calculation. To …
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
GM Morris, DS Goodsell, RS Halliday… - Journal of …, 1998 - Wiley Online Library
A novel and robust automated docking method that predicts the bound conformations of
flexible ligands to macromolecular targets has been developed and tested, in combination …
flexible ligands to macromolecular targets has been developed and tested, in combination …
Fast structure-based virtual ligand screening combining FRED, DOCK, and Surflex
A protocol was devised in which FRED, DOCK, and Surflex were combined in a multistep
virtual ligand screening (VLS) procedure to screen the pocket of four different proteins. One …
virtual ligand screening (VLS) procedure to screen the pocket of four different proteins. One …
Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs
HJ Böhm - Journal of computer-aided molecular design, 1998 - Springer
A dataset of 82 protein–ligand complexes of known 3D structure and binding constant K i
was analysed to elucidate the important factors that determine the strength of protein–ligand …
was analysed to elucidate the important factors that determine the strength of protein–ligand …
Consensus scoring for ligand/protein interactions
RD Clark, A Strizhev, JM Leonard, JF Blake… - Journal of Molecular …, 2002 - Elsevier
Several different functions have been put forward for evaluating the energetics of ligand
binding to proteins. Those employed in the DOCK, GOLD and FlexX docking programs have …
binding to proteins. Those employed in the DOCK, GOLD and FlexX docking programs have …
MedusaDock 2.0: efficient and accurate protein–ligand docking with constraints
J Wang, NV Dokholyan - Journal of chemical information and …, 2019 - ACS Publications
Molecular docking is the key ingredient of virtual drug screening, a promising and cost-
effective approach for finding new drugs. A critical limitation of this approach is the …
effective approach for finding new drugs. A critical limitation of this approach is the …
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